On Apr 11, 2012, at 2:01 PM, Jean V Adams wrote:
Alison,
Your code works fine on the first six lines of the data that you
provided.
Rumino_Reps_agreeWalign <- data.frame(
geneid = c("657313.locus_tag:RTO_08940",
"457412.251848018",
"657314.locus_tag:CK5_20630",
"657323.locus_tag:CK1_33060",
"657313.locus_tag:RTO_09690",
"471875.197297106"),
count_Conser = c(7, 1, 2, 1, 3, 0),
count_NonCons = c(5, 4, 4, 0, 0, 2),
count_ConsSubst = c(5, 3, 1, 1, 3, 1),
count_NCSubst = c(1, 0, 0, 0, 1, 1))
gene.list <- strsplit(as.character(Rumino_Reps_agreeWalign$geneid),
"\\.")
Rumino_Reps_agreeWalignTR <- transform(Rumino_Reps_agreeWalign,
taxid=do.call(rbind, gene.list))
Perhaps in later rows of the data there are cases where there is no
"." in
geneid? If not, can you provide a subset of your data that results
in the
warning? Use the dput() function.
It's not a good idea to create an object named "strsplit". That
will only
mask the function strsplit() in later runs.
There is not a problem with masking the function unless the new name
is replaced with a language object (which wasn't the case here). The
potential confusion is in minds of users. Function names are stored
separately from non-language object names so you can have a data
object named 'strsplit' and it will not mask the function 'strsplit'.
--
David.
If time is an issue, a slightly faster way to do this, after the
strsplit() function is:
Rumino_Reps_agreeWalign$geneid.prefix <- sapply(gene.list, "[", 1)
Rumino_Reps_agreeWalign$geneid.suffix <- sapply(gene.list, "[", 2)
Jean
alison waller wrote on 04/11/2012 08:23:29 AM:
Dear all,
I want to use string split to parse column names, however, I am
having
some errors that I don't understand.
I see a problem when I try to rbind the output from strsplit.
please let me know if I'm missing something obvious,
thanks,
alison
here are my commands:
strsplit<-strsplit(as.character(Rumino_Reps_agreeWalign$geneid),"\
\.")
Rumino_Reps_agreeWalignTR<-transform
(Rumino_Reps_agreeWalign,taxid=do.call(rbind,
strsplit))
Warning message:
In function (..., deparse.level = 1) :
number of columns of result is not a multiple of vector length (arg
1)
here is my data:
head(Rumino_Reps_agreeWalign)
geneid count_Conser count_NonCons
count_ConsSubst
1 657313.locus_tag:RTO_08940 7
5 5
2 457412.251848018 1
4 3
3 657314.locus_tag:CK5_20630 2
4 1
4 657323.locus_tag:CK1_33060 1
0 1
5 657313.locus_tag:RTO_09690 3
0 3
6 471875.197297106 0
2 1
count_NCSubst
1 1
2 0
3 0
4 0
5 1
6 1
here are the results from strsplit:
head(strsplit)
[[1]]
[1] "657313" "locus_tag:RTO_08940"
[[2]]
[1] "457412" "251848018"
[[3]]
[1] "657314" "locus_tag:CK5_20630"
[[4]]
[1] "657323" "locus_tag:CK1_33060"
[[5]]
[1] "657313" "locus_tag:RTO_09690"
[[6]]
[1] "471875" "197297106"
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David Winsemius, MD
West Hartford, CT
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
